Variant report

Variant	rs6921504
Chromosome Location	chr6:88058972-88058973
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:88052644..88056021-chr6:88058165..88060799,3	K562	blood:
2	chr6:88058851..88062204-chr6:88064135..88066362,3	K562	blood:

Variant related genes	Relation type
ENSG00000203872	Chromatin interaction

Extended variants
information (count: 176 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:174)

rs_ID	r²[population]
rs107689	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs107690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1080595	0.83[EUR][1000 genomes]
rs1080596	0.89[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs1201409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12176253	0.84[ASN][1000 genomes]
rs12190280	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12207825	0.87[EUR][1000 genomes]
rs12664578	0.83[EUR][1000 genomes]
rs13214153	0.80[CHB][hapmap]
rs173333	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1753153	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1753154	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs183599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1886751	0.88[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs1886752	0.89[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs1925689	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs1925695	0.88[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs1980790	0.89[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs1980792	1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2025630	0.83[EUR][1000 genomes]
rs2031518	0.82[EUR][1000 genomes]
rs2147917	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs2147918	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2147919	0.82[EUR][1000 genomes]
rs2147920	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2147921	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2182181	0.82[EUR][1000 genomes]
rs2240459	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2240460	0.82[ASN][1000 genomes]
rs242267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs242270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs242278	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs242279	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs242280	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs242281	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs242283	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs242285	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs242286	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs242287	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2474349	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2985039	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs369674	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3734187	0.84[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs373646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs376633	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3812130	0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3812132	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs381782	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3846773	0.82[ASN][1000 genomes]
rs3846774	0.82[ASN][1000 genomes]
rs3846775	0.82[ASN][1000 genomes]
rs3846776	0.84[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3857483	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs3857484	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs3857485	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3857488	0.89[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs390272	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3903920	0.88[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs3904088	0.88[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs395358	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4099964	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4110984	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs4110985	0.84[EUR][1000 genomes]
rs445434	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs446851	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs447077	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs448580	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs451089	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs451465	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs451829	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4591818	0.82[ASN][1000 genomes]
rs4605853	0.89[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs4706289	0.88[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs4707346	0.88[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs4707347	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs4707348	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs4707351	0.88[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs4707352	0.83[EUR][1000 genomes]
rs4707356	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4707357	0.84[ASN][1000 genomes]
rs4707358	0.88[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs499373	0.84[EUR][1000 genomes]
rs586771	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59322	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6454591	0.88[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs6454592	0.83[EUR][1000 genomes]
rs6454593	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs6454594	0.83[EUR][1000 genomes]
rs6454595	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6454596	0.84[ASN][1000 genomes]
rs6454597	0.83[ASN][1000 genomes]
rs6454598	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6454599	0.84[ASN][1000 genomes]
rs6454600	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6899394	0.84[ASN][1000 genomes]
rs6903219	0.92[CEU][hapmap];0.95[CHB][hapmap];0.87[EUR][1000 genomes]
rs6904310	0.88[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs6905947	0.80[CHB][hapmap]
rs6909021	0.88[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs6909200	0.88[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs6910991	0.82[ASN][1000 genomes]
rs6913721	0.83[EUR][1000 genomes]
rs6913932	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6914193	0.84[EUR][1000 genomes]
rs6914299	0.80[CHB][hapmap]
rs6916994	0.84[ASN][1000 genomes]
rs6917432	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6921007	0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6921619	0.83[EUR][1000 genomes]
rs6925648	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6926831	0.88[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs6927748	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs6932678	0.82[ASN][1000 genomes]
rs6933046	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs6933587	0.80[CHB][hapmap]
rs6934603	0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6937874	0.84[ASN][1000 genomes]
rs6940544	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7453986	0.84[ASN][1000 genomes]
rs7739034	0.84[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs7739726	0.89[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs7742478	0.88[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs7742710	1.00[JPT][hapmap]
rs7746545	0.87[EUR][1000 genomes]
rs7747129	0.85[EUR][1000 genomes]
rs7748191	0.82[EUR][1000 genomes]
rs7752485	0.88[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs7752882	0.84[EUR][1000 genomes]
rs7753030	0.84[ASN][1000 genomes]
rs7755244	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7755883	0.80[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs7757827	0.89[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs7758618	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7763365	0.83[EUR][1000 genomes]
rs7766324	0.80[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs7767449	0.83[EUR][1000 genomes]
rs7768575	0.89[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs7774603	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs7776407	0.89[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs910563	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9294371	0.80[EUR][1000 genomes]
rs9294372	0.83[EUR][1000 genomes]
rs9294379	0.80[CHB][hapmap]
rs9294381	0.80[CHB][hapmap]
rs9344690	0.94[JPT][hapmap];0.83[EUR][1000 genomes]
rs9344691	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs9344693	0.89[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs9344695	0.84[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9344696	0.84[ASN][1000 genomes]
rs9344697	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9351117	0.89[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs9351124	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9353462	0.89[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs9353463	0.83[EUR][1000 genomes]
rs9353464	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs9353465	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9353468	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9353473	0.84[ASN][1000 genomes]
rs9353483	0.87[EUR][1000 genomes]
rs9359743	0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9359748	0.96[CEU][hapmap];0.95[CHB][hapmap];0.87[EUR][1000 genomes]
rs9362398	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs9362401	0.80[EUR][1000 genomes]
rs9362408	0.83[EUR][1000 genomes]
rs9362411	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs9362415	0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9362417	0.84[ASN][1000 genomes]
rs9362427	0.86[EUR][1000 genomes]
rs9444479	0.88[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs9450634	0.82[EUR][1000 genomes]
rs9450647	0.84[ASN][1000 genomes]
rs9450650	0.80[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9450652	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018155	chr6:88049729-88272862	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv830722	chr6:88054186-88223625	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs6921504	C6orf164	cis	Esophagus Muscularis	GTEx
rs6921504	Hs.485895	cis	multi-tissue	Pritchard
rs6921504	C6orf164	cis	Artery Tibial	GTEx
rs6921504	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs6921504	C6orf164	cis	lung	GTEx
rs6921504	C6orf164	cis	Whole Blood	GTEx
rs6921504	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs6921504	C6orf163	Cis_1M	lymphoblastoid	RTeQTL
rs6921504	C6orf164	cis	Skin Sun Exposed Lower leg	GTEx
rs6921504	SLC35A1	cis	multi-tissue	Pritchard
rs6921504	C6orf164	cis	Thyroid	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88033200-88062200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr6:88039000-88068400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:88039000-88078400	Weak transcription	Fetal Stomach	stomach
4	chr6:88039400-88061200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr6:88040200-88075800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr6:88040600-88116800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:88043800-88061400	Weak transcription	Gastric	stomach
8	chr6:88043800-88068400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:88044000-88071400	Weak transcription	Fetal Muscle Leg	muscle
10	chr6:88044400-88076000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr6:88044800-88072600	Weak transcription	Adipose Nuclei	Adipose
12	chr6:88044800-88075600	Weak transcription	Fetal Lung	lung
13	chr6:88045000-88059800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:88048200-88059000	Weak transcription	Fetal Brain Female	brain
15	chr6:88049200-88066800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:88049600-88061000	Weak transcription	Left Ventricle	heart
17	chr6:88050200-88062000	Weak transcription	Fetal Heart	heart
18	chr6:88050800-88060400	Weak transcription	Osteobl	bone
19	chr6:88051200-88071200	Weak transcription	Ovary	ovary
20	chr6:88051600-88070000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr6:88054200-88059000	Weak transcription	Psoas Muscle	Psoas
22	chr6:88054600-88067400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:88054600-88068400	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr6:88054800-88075600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:88054800-88110200	Weak transcription	Primary T cells from cord blood	blood
26	chr6:88055000-88063600	Weak transcription	HSMM	muscle
27	chr6:88055000-88075800	Weak transcription	Primary B cells from cord blood	blood
28	chr6:88055200-88072800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:88057400-88073800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr6:88057600-88077200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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